Multiple sequence alignment - TraesCS3B01G139400

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS3B01G139400 chr3B 100.000 2819 0 0 1 2819 125993651 125996469 0.000000e+00 5206.0
1 TraesCS3B01G139400 chr3B 90.849 754 62 6 32 781 168700789 168701539 0.000000e+00 1003.0
2 TraesCS3B01G139400 chr3D 88.842 1882 100 36 812 2637 79621559 79623386 0.000000e+00 2211.0
3 TraesCS3B01G139400 chr3D 90.777 759 62 7 32 785 603318405 603319160 0.000000e+00 1007.0
4 TraesCS3B01G139400 chr3D 100.000 31 0 0 1 31 603318350 603318380 1.090000e-04 58.4
5 TraesCS3B01G139400 chr3A 88.889 1404 77 28 1277 2637 93702641 93704008 0.000000e+00 1655.0
6 TraesCS3B01G139400 chr3A 89.174 351 21 5 812 1158 93702313 93702650 3.360000e-114 422.0
7 TraesCS3B01G139400 chr5B 90.446 785 66 7 1 781 38864111 38864890 0.000000e+00 1026.0
8 TraesCS3B01G139400 chr5B 90.765 758 59 9 32 782 550163647 550162894 0.000000e+00 1002.0
9 TraesCS3B01G139400 chr5B 90.633 758 64 6 32 785 629689187 629689941 0.000000e+00 1000.0
10 TraesCS3B01G139400 chr5D 91.126 755 60 6 32 781 413675937 413676689 0.000000e+00 1016.0
11 TraesCS3B01G139400 chr4B 90.897 758 62 6 32 785 649630163 649630917 0.000000e+00 1011.0
12 TraesCS3B01G139400 chr4B 100.000 32 0 0 1 32 557973173 557973142 3.030000e-05 60.2
13 TraesCS3B01G139400 chr4B 100.000 31 0 0 1 31 51634481 51634511 1.090000e-04 58.4
14 TraesCS3B01G139400 chr4B 100.000 31 0 0 1 31 671901916 671901886 1.090000e-04 58.4
15 TraesCS3B01G139400 chr1B 90.897 758 62 6 32 785 47511278 47512032 0.000000e+00 1011.0
16 TraesCS3B01G139400 chr6D 90.861 755 64 4 32 782 469366066 469365313 0.000000e+00 1007.0
17 TraesCS3B01G139400 chr2D 90.521 749 60 8 41 782 71920170 71919426 0.000000e+00 979.0
18 TraesCS3B01G139400 chr2D 100.000 31 0 0 1 31 58657770 58657800 1.090000e-04 58.4
19 TraesCS3B01G139400 chr4A 100.000 31 0 0 1 31 652092398 652092368 1.090000e-04 58.4
20 TraesCS3B01G139400 chr2B 97.143 35 0 1 1 34 131825981 131826015 1.090000e-04 58.4


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3B01G139400 chr3B 125993651 125996469 2818 False 5206.0 5206 100.0000 1 2819 1 chr3B.!!$F1 2818
1 TraesCS3B01G139400 chr3B 168700789 168701539 750 False 1003.0 1003 90.8490 32 781 1 chr3B.!!$F2 749
2 TraesCS3B01G139400 chr3D 79621559 79623386 1827 False 2211.0 2211 88.8420 812 2637 1 chr3D.!!$F1 1825
3 TraesCS3B01G139400 chr3D 603318350 603319160 810 False 532.7 1007 95.3885 1 785 2 chr3D.!!$F2 784
4 TraesCS3B01G139400 chr3A 93702313 93704008 1695 False 1038.5 1655 89.0315 812 2637 2 chr3A.!!$F1 1825
5 TraesCS3B01G139400 chr5B 38864111 38864890 779 False 1026.0 1026 90.4460 1 781 1 chr5B.!!$F1 780
6 TraesCS3B01G139400 chr5B 550162894 550163647 753 True 1002.0 1002 90.7650 32 782 1 chr5B.!!$R1 750
7 TraesCS3B01G139400 chr5B 629689187 629689941 754 False 1000.0 1000 90.6330 32 785 1 chr5B.!!$F2 753
8 TraesCS3B01G139400 chr5D 413675937 413676689 752 False 1016.0 1016 91.1260 32 781 1 chr5D.!!$F1 749
9 TraesCS3B01G139400 chr4B 649630163 649630917 754 False 1011.0 1011 90.8970 32 785 1 chr4B.!!$F2 753
10 TraesCS3B01G139400 chr1B 47511278 47512032 754 False 1011.0 1011 90.8970 32 785 1 chr1B.!!$F1 753
11 TraesCS3B01G139400 chr6D 469365313 469366066 753 True 1007.0 1007 90.8610 32 782 1 chr6D.!!$R1 750
12 TraesCS3B01G139400 chr2D 71919426 71920170 744 True 979.0 979 90.5210 41 782 1 chr2D.!!$R1 741

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
559 593 0.033504 GCGTGGGAGTGAAGTTGAGA 59.966 55.0 0.0 0.0 0.0 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2448 2538 0.1078 CCAGCACCAGTCCATCTCAG 60.108 60.0 0.0 0.0 0.0 3.35 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
83 108 1.140312 TCACCTCTTCACCCAAGCTT 58.860 50.000 0.00 0.00 31.26 3.74
88 113 2.553904 CCTCTTCACCCAAGCTTGATGT 60.554 50.000 28.05 20.02 31.26 3.06
186 211 3.561120 GACCGGGGCAACATGTCCA 62.561 63.158 6.32 0.00 45.98 4.02
210 235 0.994995 CACGCCATCGAACTTCAGAG 59.005 55.000 0.00 0.00 39.41 3.35
227 253 2.124570 GCTGACACCCCGCATGAT 60.125 61.111 0.00 0.00 0.00 2.45
244 276 1.078637 ATGACGACGTCGGAGGAGA 60.079 57.895 37.89 17.12 44.95 3.71
327 361 1.745115 GCATAGACAACCGCCTGCA 60.745 57.895 0.00 0.00 0.00 4.41
342 376 1.645034 CTGCACGTACTCCTGAATGG 58.355 55.000 0.00 0.00 37.10 3.16
352 386 2.108952 ACTCCTGAATGGCAAAACCTCT 59.891 45.455 0.00 0.00 40.22 3.69
353 387 3.160269 CTCCTGAATGGCAAAACCTCTT 58.840 45.455 0.00 0.00 40.22 2.85
390 424 2.669569 AGACAACGCCGCAGCAAT 60.670 55.556 0.00 0.00 39.83 3.56
416 450 1.204467 CAGAGCAGAAGGAGAGACACC 59.796 57.143 0.00 0.00 0.00 4.16
422 456 1.150135 AGAAGGAGAGACACCCCTGAA 59.850 52.381 0.00 0.00 0.00 3.02
485 519 0.526662 ACGTTGTCGATCTGAGGGAC 59.473 55.000 0.00 4.46 40.62 4.46
490 524 1.818363 TCGATCTGAGGGACCGACG 60.818 63.158 0.00 0.00 0.00 5.12
535 569 2.034879 CGCCGCCATGAAAGACACT 61.035 57.895 0.00 0.00 0.00 3.55
541 575 1.503542 CATGAAAGACACTGCCGGC 59.496 57.895 22.73 22.73 0.00 6.13
559 593 0.033504 GCGTGGGAGTGAAGTTGAGA 59.966 55.000 0.00 0.00 0.00 3.27
582 616 0.107410 ATTTATTCGTCCAGGCGCCA 60.107 50.000 31.54 4.59 0.00 5.69
630 664 6.259387 CCACGACTTATAAATCCAAACCCTAC 59.741 42.308 0.00 0.00 0.00 3.18
644 678 0.183014 CCCTACCTACAGAGCGGAGA 59.817 60.000 0.00 0.00 0.00 3.71
745 780 3.161866 GAGGAAATAGATCGCCTCTCCT 58.838 50.000 0.00 9.20 42.81 3.69
746 781 4.337145 GAGGAAATAGATCGCCTCTCCTA 58.663 47.826 0.00 0.00 42.81 2.94
747 782 4.340617 AGGAAATAGATCGCCTCTCCTAG 58.659 47.826 5.05 0.00 35.28 3.02
748 783 4.043561 AGGAAATAGATCGCCTCTCCTAGA 59.956 45.833 0.00 0.00 35.28 2.43
785 820 1.143401 GGCTAGGGTAGGAACACGC 59.857 63.158 0.00 0.00 32.69 5.34
786 821 1.328430 GGCTAGGGTAGGAACACGCT 61.328 60.000 0.00 0.00 43.41 5.07
787 822 1.396653 GCTAGGGTAGGAACACGCTA 58.603 55.000 0.00 0.00 41.46 4.26
788 823 1.962100 GCTAGGGTAGGAACACGCTAT 59.038 52.381 0.00 0.00 41.46 2.97
789 824 2.364647 GCTAGGGTAGGAACACGCTATT 59.635 50.000 0.00 0.00 41.46 1.73
790 825 2.981859 AGGGTAGGAACACGCTATTG 57.018 50.000 0.00 0.00 39.68 1.90
791 826 1.485066 AGGGTAGGAACACGCTATTGG 59.515 52.381 0.00 0.00 39.68 3.16
792 827 1.208776 GGGTAGGAACACGCTATTGGT 59.791 52.381 0.00 0.00 0.00 3.67
793 828 2.355412 GGGTAGGAACACGCTATTGGTT 60.355 50.000 0.00 0.00 0.00 3.67
794 829 3.340928 GGTAGGAACACGCTATTGGTTT 58.659 45.455 0.00 0.00 0.00 3.27
795 830 3.754850 GGTAGGAACACGCTATTGGTTTT 59.245 43.478 0.00 0.00 0.00 2.43
796 831 4.216902 GGTAGGAACACGCTATTGGTTTTT 59.783 41.667 0.00 0.00 0.00 1.94
898 935 4.378253 GCTCTGTTTGCTCTCAGATTGTTC 60.378 45.833 5.95 0.00 39.48 3.18
927 964 1.134670 CCGGATTCCTCAGAGACCAAC 60.135 57.143 0.00 0.00 0.00 3.77
951 988 3.131396 GGCTATATCCAACGTTCCTGTG 58.869 50.000 0.00 0.00 0.00 3.66
966 1004 1.953231 CTGTGCTCCCTGATCAGCGA 61.953 60.000 17.76 13.46 38.59 4.93
989 1027 4.491409 GGAAGAAGGCCCGCCCTC 62.491 72.222 0.00 0.00 45.62 4.30
990 1028 3.403558 GAAGAAGGCCCGCCCTCT 61.404 66.667 0.00 0.87 45.62 3.69
991 1029 3.689002 GAAGAAGGCCCGCCCTCTG 62.689 68.421 7.61 0.00 45.62 3.35
1016 1054 4.838152 GATGCCTCCGCCGCTGAA 62.838 66.667 0.00 0.00 0.00 3.02
1032 1070 2.437359 AAGGACATGCTGCCGCTC 60.437 61.111 0.70 0.00 36.97 5.03
1110 1149 2.790791 CCAAAGCAAACGCCACCCA 61.791 57.895 0.00 0.00 0.00 4.51
1215 1257 3.209091 CCTCCAGGTCCAGTACGAT 57.791 57.895 0.00 0.00 0.00 3.73
1255 1297 3.858868 GACCGCACGTTCCTGCTCA 62.859 63.158 0.00 0.00 34.77 4.26
1267 1309 2.525629 TGCTCAACGACCCCAGGA 60.526 61.111 0.00 0.00 0.00 3.86
1310 1352 4.444838 CCGCGACGGGATCAACCA 62.445 66.667 8.23 0.00 44.15 3.67
1668 1719 2.865308 CTGCCATGCTCACACACG 59.135 61.111 0.00 0.00 0.00 4.49
1949 2003 3.430453 TGGAAATGCTAAAAGGGGAGTG 58.570 45.455 0.00 0.00 0.00 3.51
2112 2184 6.854886 GTGTTCACACAAAAGAAGAAGAAC 57.145 37.500 5.16 0.00 45.75 3.01
2113 2185 6.378582 GTGTTCACACAAAAGAAGAAGAACA 58.621 36.000 5.16 0.00 45.75 3.18
2114 2186 6.861055 GTGTTCACACAAAAGAAGAAGAACAA 59.139 34.615 5.16 0.00 43.62 2.83
2115 2187 7.381139 GTGTTCACACAAAAGAAGAAGAACAAA 59.619 33.333 5.16 0.00 43.62 2.83
2116 2188 7.923344 TGTTCACACAAAAGAAGAAGAACAAAA 59.077 29.630 0.00 0.00 40.50 2.44
2117 2189 8.760569 GTTCACACAAAAGAAGAAGAACAAAAA 58.239 29.630 0.00 0.00 35.47 1.94
2388 2478 1.467920 GGGAGCTCCATGTTTTGAGG 58.532 55.000 33.29 0.00 37.91 3.86
2394 2484 1.135315 CCATGTTTTGAGGCGAGCG 59.865 57.895 0.00 0.00 0.00 5.03
2424 2514 0.029834 GCCTAACGAACGCGAGGATA 59.970 55.000 15.93 0.00 41.64 2.59
2431 2521 0.653897 GAACGCGAGGATACGTCGAG 60.654 60.000 15.93 14.71 42.68 4.04
2448 2538 2.735663 TCGAGACGTGTAGACAGAGTTC 59.264 50.000 0.00 0.00 0.00 3.01
2486 2589 1.691434 GGGAGGAGAGCGATGAAGAAT 59.309 52.381 0.00 0.00 0.00 2.40
2602 2730 0.687354 GTGGACTGGATGGTGACTGT 59.313 55.000 0.00 0.00 0.00 3.55
2606 2734 0.035881 ACTGGATGGTGACTGTGCAG 59.964 55.000 7.45 7.45 39.59 4.41
2623 2751 0.443869 CAGTGACGATTTTGCCCTCG 59.556 55.000 0.00 0.00 40.62 4.63
2637 2765 0.729140 CCCTCGCGCATGTTGTTTTC 60.729 55.000 8.75 0.00 0.00 2.29
2638 2766 0.729140 CCTCGCGCATGTTGTTTTCC 60.729 55.000 8.75 0.00 0.00 3.13
2639 2767 0.238289 CTCGCGCATGTTGTTTTCCT 59.762 50.000 8.75 0.00 0.00 3.36
2640 2768 0.665835 TCGCGCATGTTGTTTTCCTT 59.334 45.000 8.75 0.00 0.00 3.36
2641 2769 1.066303 TCGCGCATGTTGTTTTCCTTT 59.934 42.857 8.75 0.00 0.00 3.11
2642 2770 2.290916 TCGCGCATGTTGTTTTCCTTTA 59.709 40.909 8.75 0.00 0.00 1.85
2643 2771 3.057876 TCGCGCATGTTGTTTTCCTTTAT 60.058 39.130 8.75 0.00 0.00 1.40
2644 2772 4.154375 TCGCGCATGTTGTTTTCCTTTATA 59.846 37.500 8.75 0.00 0.00 0.98
2645 2773 4.854291 CGCGCATGTTGTTTTCCTTTATAA 59.146 37.500 8.75 0.00 0.00 0.98
2646 2774 5.343593 CGCGCATGTTGTTTTCCTTTATAAA 59.656 36.000 8.75 0.00 0.00 1.40
2647 2775 6.034470 CGCGCATGTTGTTTTCCTTTATAAAT 59.966 34.615 8.75 0.00 0.00 1.40
2648 2776 7.391016 GCGCATGTTGTTTTCCTTTATAAATC 58.609 34.615 0.30 0.00 0.00 2.17
2649 2777 7.275560 GCGCATGTTGTTTTCCTTTATAAATCT 59.724 33.333 0.30 0.00 0.00 2.40
2650 2778 8.798153 CGCATGTTGTTTTCCTTTATAAATCTC 58.202 33.333 0.00 0.00 0.00 2.75
2651 2779 9.860898 GCATGTTGTTTTCCTTTATAAATCTCT 57.139 29.630 0.00 0.00 0.00 3.10
2654 2782 9.691362 TGTTGTTTTCCTTTATAAATCTCTTGC 57.309 29.630 0.00 0.00 0.00 4.01
2655 2783 9.691362 GTTGTTTTCCTTTATAAATCTCTTGCA 57.309 29.630 0.00 0.00 0.00 4.08
2663 2791 9.455847 CCTTTATAAATCTCTTGCAATGTTAGC 57.544 33.333 0.00 0.00 0.00 3.09
2668 2796 9.956720 ATAAATCTCTTGCAATGTTAGCATAAC 57.043 29.630 0.00 0.00 42.33 1.89
2669 2797 7.395190 AATCTCTTGCAATGTTAGCATAACA 57.605 32.000 0.00 4.94 42.33 2.41
2670 2798 7.578310 ATCTCTTGCAATGTTAGCATAACAT 57.422 32.000 0.00 8.92 42.33 2.71
2671 2799 6.788243 TCTCTTGCAATGTTAGCATAACATG 58.212 36.000 14.17 10.21 42.33 3.21
2672 2800 6.598850 TCTCTTGCAATGTTAGCATAACATGA 59.401 34.615 14.17 7.40 42.33 3.07
2673 2801 6.554419 TCTTGCAATGTTAGCATAACATGAC 58.446 36.000 14.17 10.51 42.33 3.06
2674 2802 5.893897 TGCAATGTTAGCATAACATGACA 57.106 34.783 14.17 12.44 40.43 3.58
2675 2803 6.453926 TGCAATGTTAGCATAACATGACAT 57.546 33.333 14.17 0.00 40.43 3.06
2676 2804 6.865411 TGCAATGTTAGCATAACATGACATT 58.135 32.000 14.17 0.00 40.43 2.71
2677 2805 7.994194 TGCAATGTTAGCATAACATGACATTA 58.006 30.769 14.17 0.00 40.43 1.90
2678 2806 8.465201 TGCAATGTTAGCATAACATGACATTAA 58.535 29.630 14.17 0.00 40.43 1.40
2679 2807 9.467258 GCAATGTTAGCATAACATGACATTAAT 57.533 29.630 14.17 0.00 40.43 1.40
2706 2834 7.921041 AGAAAAGATGGACTACTATGGATCA 57.079 36.000 0.00 0.00 0.00 2.92
2707 2835 8.503428 AGAAAAGATGGACTACTATGGATCAT 57.497 34.615 0.00 0.00 0.00 2.45
2708 2836 8.943085 AGAAAAGATGGACTACTATGGATCATT 58.057 33.333 0.00 0.00 0.00 2.57
2709 2837 9.213799 GAAAAGATGGACTACTATGGATCATTC 57.786 37.037 0.00 0.00 0.00 2.67
2710 2838 7.862274 AAGATGGACTACTATGGATCATTCA 57.138 36.000 0.00 0.00 0.00 2.57
2711 2839 7.862274 AGATGGACTACTATGGATCATTCAA 57.138 36.000 0.00 0.00 0.00 2.69
2712 2840 8.267620 AGATGGACTACTATGGATCATTCAAA 57.732 34.615 0.00 0.00 0.00 2.69
2713 2841 8.717717 AGATGGACTACTATGGATCATTCAAAA 58.282 33.333 0.00 0.00 0.00 2.44
2714 2842 8.682936 ATGGACTACTATGGATCATTCAAAAC 57.317 34.615 0.00 0.00 0.00 2.43
2715 2843 7.629157 TGGACTACTATGGATCATTCAAAACA 58.371 34.615 0.00 0.00 0.00 2.83
2716 2844 8.106462 TGGACTACTATGGATCATTCAAAACAA 58.894 33.333 0.00 0.00 0.00 2.83
2717 2845 9.125026 GGACTACTATGGATCATTCAAAACAAT 57.875 33.333 0.00 0.00 0.00 2.71
2750 2878 9.490663 GACACTTAAAGTATCAACATATTGTGC 57.509 33.333 0.00 0.00 37.11 4.57
2751 2879 9.231297 ACACTTAAAGTATCAACATATTGTGCT 57.769 29.630 0.00 0.00 37.11 4.40
2758 2886 9.830975 AAGTATCAACATATTGTGCTATGTACA 57.169 29.630 0.00 0.00 40.57 2.90
2759 2887 9.830975 AGTATCAACATATTGTGCTATGTACAA 57.169 29.630 0.00 3.95 40.57 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
83 108 1.153309 CAGCGATGGAGCCACATCA 60.153 57.895 15.84 0.00 45.87 3.07
88 113 0.462581 GTTGATCAGCGATGGAGCCA 60.463 55.000 0.00 0.00 38.01 4.75
186 211 2.430382 AAGTTCGATGGCGTGTCCGT 62.430 55.000 0.00 0.00 38.98 4.69
210 235 2.124570 ATCATGCGGGGTGTCAGC 60.125 61.111 0.00 0.00 37.09 4.26
227 253 0.886043 TTTCTCCTCCGACGTCGTCA 60.886 55.000 33.49 20.00 37.74 4.35
244 276 2.736670 AGGCTGACAGTTCTGGTTTT 57.263 45.000 3.99 0.00 0.00 2.43
300 334 3.002791 CGGTTGTCTATGCAAGTGACAT 58.997 45.455 16.64 0.00 39.92 3.06
327 361 2.812011 GTTTTGCCATTCAGGAGTACGT 59.188 45.455 0.00 0.00 41.22 3.57
352 386 0.948623 CGACGTCATGGTGGAGCAAA 60.949 55.000 17.16 0.00 0.00 3.68
353 387 1.374125 CGACGTCATGGTGGAGCAA 60.374 57.895 17.16 0.00 0.00 3.91
383 417 2.413142 GCTCTGTCCCCATTGCTGC 61.413 63.158 0.00 0.00 0.00 5.25
390 424 0.906756 CTCCTTCTGCTCTGTCCCCA 60.907 60.000 0.00 0.00 0.00 4.96
416 450 4.821589 GCGGCGACTCCTTCAGGG 62.822 72.222 12.98 0.00 35.41 4.45
437 471 1.003839 GGATGGTGTTGGCGAGACA 60.004 57.895 4.23 0.00 0.00 3.41
485 519 2.158959 GGCATCGTGTCTTCGTCGG 61.159 63.158 0.00 0.00 0.00 4.79
490 524 2.349886 GAGTTGATGGCATCGTGTCTTC 59.650 50.000 21.65 9.94 0.00 2.87
541 575 1.068588 TGTCTCAACTTCACTCCCACG 59.931 52.381 0.00 0.00 0.00 4.94
551 585 6.464222 TGGACGAATAAATCTGTCTCAACTT 58.536 36.000 0.00 0.00 34.30 2.66
559 593 2.550978 CGCCTGGACGAATAAATCTGT 58.449 47.619 0.00 0.00 34.06 3.41
582 616 3.566210 CGTTGGGGTGGTGGGAGT 61.566 66.667 0.00 0.00 0.00 3.85
612 646 8.626917 TCTGTAGGTAGGGTTTGGATTTATAA 57.373 34.615 0.00 0.00 0.00 0.98
630 664 1.202580 CCCATTTCTCCGCTCTGTAGG 60.203 57.143 0.00 0.00 0.00 3.18
717 751 3.056465 GGCGATCTATTTCCTCCGATCTT 60.056 47.826 0.00 0.00 32.22 2.40
745 780 3.065306 CCACCACCAGGCGTTCTA 58.935 61.111 0.00 0.00 39.06 2.10
746 781 4.643387 GCCACCACCAGGCGTTCT 62.643 66.667 0.00 0.00 43.15 3.01
793 828 2.642154 TCCGAGGCCAACAGTAAAAA 57.358 45.000 5.01 0.00 0.00 1.94
794 829 2.432444 CATCCGAGGCCAACAGTAAAA 58.568 47.619 5.01 0.00 0.00 1.52
795 830 1.948611 GCATCCGAGGCCAACAGTAAA 60.949 52.381 5.01 0.00 0.00 2.01
796 831 0.392461 GCATCCGAGGCCAACAGTAA 60.392 55.000 5.01 0.00 0.00 2.24
797 832 1.220749 GCATCCGAGGCCAACAGTA 59.779 57.895 5.01 0.00 0.00 2.74
798 833 2.045926 GCATCCGAGGCCAACAGT 60.046 61.111 5.01 0.00 0.00 3.55
799 834 1.442526 GATGCATCCGAGGCCAACAG 61.443 60.000 16.23 0.00 0.00 3.16
800 835 1.451927 GATGCATCCGAGGCCAACA 60.452 57.895 16.23 0.00 0.00 3.33
801 836 2.189499 GGATGCATCCGAGGCCAAC 61.189 63.158 29.34 4.01 37.19 3.77
802 837 2.192979 GGATGCATCCGAGGCCAA 59.807 61.111 29.34 0.00 37.19 4.52
927 964 0.782384 GAACGTTGGATATAGCCGCG 59.218 55.000 18.16 18.16 35.83 6.46
1012 1050 2.758089 GCGGCAGCATGTCCTTCAG 61.758 63.158 3.18 0.00 37.49 3.02
1205 1247 1.712018 CGCGTCCTCATCGTACTGGA 61.712 60.000 0.00 0.00 0.00 3.86
1210 1252 3.896133 GGGCGCGTCCTCATCGTA 61.896 66.667 25.46 0.00 34.39 3.43
1255 1297 0.767060 AAGAAGGTCCTGGGGTCGTT 60.767 55.000 0.00 0.00 0.00 3.85
1259 1301 1.918800 CGGAAGAAGGTCCTGGGGT 60.919 63.158 0.00 0.00 35.31 4.95
1267 1309 4.083862 GCGGCTCCGGAAGAAGGT 62.084 66.667 5.23 0.00 40.19 3.50
1301 1343 1.293924 CGTGAGCATCTGGTTGATCC 58.706 55.000 0.00 0.00 34.92 3.36
1668 1719 4.681978 AGCCAGCGGACGTGGAAC 62.682 66.667 14.45 2.01 37.23 3.62
1819 1872 4.949856 TCTTTTAGCAATCAGGGTCCAATC 59.050 41.667 0.00 0.00 0.00 2.67
1857 1910 9.661187 GAAATGTCTATATGCTGAATGAACAAG 57.339 33.333 0.00 0.00 0.00 3.16
1942 1996 1.077716 CATTTCCCCGTCACTCCCC 60.078 63.158 0.00 0.00 0.00 4.81
1949 2003 1.757682 TACATTGCCATTTCCCCGTC 58.242 50.000 0.00 0.00 0.00 4.79
2009 2067 6.131264 TGGCAGATTATGGAGTGAAATGAAT 58.869 36.000 0.00 0.00 0.00 2.57
2012 2070 5.840243 TTGGCAGATTATGGAGTGAAATG 57.160 39.130 0.00 0.00 0.00 2.32
2013 2071 5.954150 AGTTTGGCAGATTATGGAGTGAAAT 59.046 36.000 0.00 0.00 0.00 2.17
2019 2077 5.192927 TGGTTAGTTTGGCAGATTATGGAG 58.807 41.667 0.00 0.00 0.00 3.86
2221 2293 1.107114 AGACGAGGCTGTACATCCTG 58.893 55.000 22.67 15.96 31.71 3.86
2431 2521 3.747010 TCTCAGAACTCTGTCTACACGTC 59.253 47.826 6.61 0.00 44.12 4.34
2441 2531 2.830923 ACCAGTCCATCTCAGAACTCTG 59.169 50.000 0.00 0.00 45.08 3.35
2448 2538 0.107800 CCAGCACCAGTCCATCTCAG 60.108 60.000 0.00 0.00 0.00 3.35
2486 2589 3.804786 TTTAACTACCGGCATCGATCA 57.195 42.857 0.00 0.00 39.00 2.92
2602 2730 0.537143 AGGGCAAAATCGTCACTGCA 60.537 50.000 0.00 0.00 36.50 4.41
2606 2734 1.134694 GCGAGGGCAAAATCGTCAC 59.865 57.895 0.00 0.00 40.97 3.67
2623 2751 6.698359 TTTATAAAGGAAAACAACATGCGC 57.302 33.333 0.00 0.00 0.00 6.09
2637 2765 9.455847 GCTAACATTGCAAGAGATTTATAAAGG 57.544 33.333 4.94 0.00 0.00 3.11
2642 2770 9.956720 GTTATGCTAACATTGCAAGAGATTTAT 57.043 29.630 4.94 0.00 44.01 1.40
2643 2771 8.955388 TGTTATGCTAACATTGCAAGAGATTTA 58.045 29.630 4.94 0.00 44.01 1.40
2644 2772 7.829725 TGTTATGCTAACATTGCAAGAGATTT 58.170 30.769 4.94 0.00 44.01 2.17
2645 2773 7.395190 TGTTATGCTAACATTGCAAGAGATT 57.605 32.000 4.94 0.00 44.01 2.40
2646 2774 7.283807 TCATGTTATGCTAACATTGCAAGAGAT 59.716 33.333 4.94 0.00 44.01 2.75
2647 2775 6.598850 TCATGTTATGCTAACATTGCAAGAGA 59.401 34.615 4.94 8.02 44.01 3.10
2648 2776 6.690098 GTCATGTTATGCTAACATTGCAAGAG 59.310 38.462 4.94 2.40 44.01 2.85
2649 2777 6.150809 TGTCATGTTATGCTAACATTGCAAGA 59.849 34.615 4.94 8.97 44.01 3.02
2650 2778 6.324042 TGTCATGTTATGCTAACATTGCAAG 58.676 36.000 4.94 0.00 44.01 4.01
2651 2779 6.264841 TGTCATGTTATGCTAACATTGCAA 57.735 33.333 0.00 0.00 44.01 4.08
2652 2780 5.893897 TGTCATGTTATGCTAACATTGCA 57.106 34.783 14.86 13.61 44.95 4.08
2653 2781 8.854979 TTAATGTCATGTTATGCTAACATTGC 57.145 30.769 14.86 12.02 38.69 3.56
2680 2808 9.434275 TGATCCATAGTAGTCCATCTTTTCTAA 57.566 33.333 0.00 0.00 0.00 2.10
2681 2809 9.607333 ATGATCCATAGTAGTCCATCTTTTCTA 57.393 33.333 0.00 0.00 0.00 2.10
2682 2810 7.921041 TGATCCATAGTAGTCCATCTTTTCT 57.079 36.000 0.00 0.00 0.00 2.52
2683 2811 9.213799 GAATGATCCATAGTAGTCCATCTTTTC 57.786 37.037 0.00 0.00 0.00 2.29
2684 2812 8.717717 TGAATGATCCATAGTAGTCCATCTTTT 58.282 33.333 0.00 0.00 0.00 2.27
2685 2813 8.267620 TGAATGATCCATAGTAGTCCATCTTT 57.732 34.615 0.00 0.00 0.00 2.52
2686 2814 7.862274 TGAATGATCCATAGTAGTCCATCTT 57.138 36.000 0.00 0.00 0.00 2.40
2687 2815 7.862274 TTGAATGATCCATAGTAGTCCATCT 57.138 36.000 0.00 0.00 0.00 2.90
2688 2816 8.778358 GTTTTGAATGATCCATAGTAGTCCATC 58.222 37.037 0.00 0.00 0.00 3.51
2689 2817 8.274322 TGTTTTGAATGATCCATAGTAGTCCAT 58.726 33.333 0.00 0.00 0.00 3.41
2690 2818 7.629157 TGTTTTGAATGATCCATAGTAGTCCA 58.371 34.615 0.00 0.00 0.00 4.02
2691 2819 8.506168 TTGTTTTGAATGATCCATAGTAGTCC 57.494 34.615 0.00 0.00 0.00 3.85
2724 2852 9.490663 GCACAATATGTTGATACTTTAAGTGTC 57.509 33.333 13.72 13.72 38.71 3.67
2725 2853 9.231297 AGCACAATATGTTGATACTTTAAGTGT 57.769 29.630 9.40 0.04 38.71 3.55
2732 2860 9.830975 TGTACATAGCACAATATGTTGATACTT 57.169 29.630 9.40 0.00 42.40 2.24
2733 2861 9.830975 TTGTACATAGCACAATATGTTGATACT 57.169 29.630 9.40 5.58 42.40 2.12
2740 2868 9.627123 ACCTTTATTGTACATAGCACAATATGT 57.373 29.630 0.00 4.88 44.28 2.29


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.